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help - hoslem.test

2 messages · PIKAL Petr, Luciane Maria Pilotto

Original
PIKAL Petr
# 
Hi

thanks for data.

na.exclude does not excludes NA values. Actually it computes result without considering NAs but keeps those NA values in propper positions so that the result has the same length as input

Instead of several ifelse you can use

q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1

fitted values start with NA values
1241         1242         1243         1244         1245         1246
          NA           NA 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
        1247         1248         1256         1268
2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11

which obviously hoslem.test is not adapted to.
you can use glm without na.action and your fitted values will be without NA.
1243         1244         1245         1246         1247         1248
2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
        1256         1268
2.143345e-11 2.143345e-11

however
tp1$q131 does not exist
NULL
So again, test throws error.

Maybe you wanted
Hosmer and Lemeshow goodness of fit (GOF) test

data:  na.omit(id3$q131), fitted(tp1)
X-squared = NaN, df = 8, p-value = NA

Warning message:
In Ops.factor(1, y) : ?-? not meaningful for factors

However q131 is factor (actually you changed it to factor)

If I change it to numeric
Hosmer and Lemeshow goodness of fit (GOF) test

data:  na.omit(id3$q131), fitted(tp1)
X-squared = NaN, df = 8, p-value = NA

hoslem test works - at least it does not throw errors.

So best way for you would be to understand basic differences in object types (numeric, factor, ....) by reading R intro and think about what hoslem test needs as an input.

Cheers
Petr
<snip>
Instead of several ifelse you can use

q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1
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Luciane Maria Pilotto
# 
Hi

Thanks for the help!
I used the following commands to run the test hoslem:

rl<-id3[,c("q06", "q08", "q10", "q11", "q12", "q13", "q14", "sexo", "edcat", "rendacat", "cpod", 
          "getario", "bwgr_et")]#select only variables of interest
dim(rl)#[1] 22843    12
attach(rl)

q131 <- as.numeric(cut(rl$q13,c(0,1.5,5)))-1
rl<-cbind(rl,q131)

rlna<-rl[complete.cases(rl),]#exclude NA

tpna <- glm(q131 ~ q11 + q10+rendacat+q12 + q08+q06 + q14, 
            family = binomial(link = "logit"), data=rlna)
hoslem.test(rlna$q131, fitted(tpna), g=10)

Thanks
Luciane

--------------------------------------------
Em seg, 4/5/15, PIKAL Petr <petr.pikal at precheza.cz> escreveu:

 Assunto: RE: [R] help - hoslem.test

t.org" <r-help at r-project.org>
 Data: Segunda-feira, 4 de Maio de 2015, 10:24

 Hi

 thanks for data.

 na.exclude does not excludes NA values. Actually it computes
 result without considering NAs but keeps those NA values in
 propper positions so that the result has the same length as
 input

 Instead of several ifelse you can use

 q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1

 fitted values start with NA values

 > fitted(tp1)
 ? ? ? ? 1241? ? ?
 ???1242? ? ?
 ???1243? ? ?
 ???1244? ? ?
 ???1245? ? ?
 ???1246
 ? ? ? ? ? NA? ? ?
 ? ???NA 2.143345e-11 2.143345e-11
 2.143345e-11 2.143345e-11
 ? ? ? ? 1247? ? ?
 ???1248? ? ?
 ???1256? ? ?
 ???1268
 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11

 which obviously hoslem.test is not adapted to.

 >
 > #Error in quantile.default(yhat, probs = seq(0, 1,
 1/g)) :
 >? # missing values and NaN's not allowed if 'na.rm'
 is FALSE

 you can use glm without na.action and your fitted values
 will be without NA.

 > tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+
 q14, family = binomial(link = "logit"), data=id3)
 > fitted(tp1)
 ? ? ? ? 1243? ? ?
 ???1244? ? ?
 ???1245? ? ?
 ???1246? ? ?
 ???1247? ? ?
 ???1248
 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
 2.143345e-11 2.143345e-11
 ? ? ? ? 1256? ? ?
 ???1268
 2.143345e-11 2.143345e-11

 however
 tp1$q131 does not exist

 > tp1$q131
 NULL
 So again, test throws error.

 Maybe you wanted

 > hoslem.test(na.omit(id3$q131), fitted(tp1), g=10)

 ? ? ? ? Hosmer and Lemeshow goodness of
 fit (GOF) test

 data:? na.omit(id3$q131), fitted(tp1)
 X-squared = NaN, df = 8, p-value = NA

 Warning message:
 In Ops.factor(1, y) : ?-? not meaningful for factors

 However q131 is factor (actually you changed it to factor)

 If I change it to numeric

 > id3$q131<-q131
 > tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+
 q14, family = binomial(link = "logit"), data=id3)
 > hoslem.test(na.omit(id3$q131), fitted(tp1), g=10)

 ? ? ? ? Hosmer and Lemeshow goodness of
 fit (GOF) test

 data:? na.omit(id3$q131), fitted(tp1)
 X-squared = NaN, df = 8, p-value = NA

 hoslem test works - at least it does not throw errors.

 So best way for you would be to understand basic differences
 in object types (numeric, factor, ....) by reading R intro
 and think about what hoslem test needs as an input.

 Cheers
 Petr

 > -----Original Message-----

 > Sent: Monday, May 04, 2015 2:46 PM
 > To: r-help at r-project.org;
 PIKAL Petr
 > Subject: RE: [R] help - hoslem.test
 >
 > Hi
 >
 > I'm trying to make a reproducible example using the
 command "dput" as
 > fallows.
 >
 > The problem occurs when running the test of Hosmer and
 Lemeshow
 > (hoslem.test) for residuals gives error. I'm using the
 command
 > "na.action" to exclude the NA values.
 >
 > Thanks,
 > Luciane
 >
 > ###############################################
 >
 > load(file.choose())#dataframe:"id3.rda"
 > attach(id3)
 >

 <snip>

 >
 > #create binary outcome variable (q13) (transformando
 q13 em bin?ria)
 >
 q131<-ifelse(q13==1,0,ifelse(q13==2,1,ifelse(q13==3,1,
 > ifelse(q13==4,1,ifelse(q13==5,1,NA)))))

 Instead of several ifelse you can use

 q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1

 > id3<-cbind(id3,q131)
 > id3$q131 <- as.factor(id3$q131)
 >
 > str(id3)
 >
 > tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+
 q14, family =
 > binomial(link = "logit"), data=id3,
 na.action="na.exclude")
 > tp1
 >
 > library(ResourceSelection)
 > hoslem.test(tp1$q131, fitted(tp1), g=10)
 >
 >
 >
 >
 > --------------------------------------------
 > Em sex, 1/5/15, PIKAL Petr <petr.pikal at precheza.cz>
 escreveu:
 >
 >? Assunto: RE: [R] help - hoslem.test

 "r-help at r-
 > project.org" <r-help at r-project.org>
 >? Data: Sexta-feira, 1 de Maio de 2015, 3:59
 >
 >? Hi
 >
 >? > -----Original Message-----

 >? > Sent: Friday, May 01, 2015 12:49 AM
 >? > To: PIKAL Petr; r-help at r-project.org;
 >? John Kane
 >? > Subject: Re: [R] help -
 >? hoslem.test
 >? >
 >? > Ok, in
 >? dropbox link below you can download the bank.
 >? > (https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0)
 >
 >? No. Not everybody is alowed to
 >? use dropbox. Try to post result of
 >
 >? dput(id3)
 >
 >? directly to your post.
 >
 >? Cheers
 >? Petr
 >
 >? >
 >? > I change the script
 >? following the suggestions, but the error
 persists.
 >? > I used the the na.action command to delete
 >? the lost values.
 >? >
 >? >
 >
 >
 #######################################################################
 >? >
 >? >
 >? load("id3.rda")
 >? >
 >? attach(id3)
 >? >
 >? >
 >? #transformando q13 em bin?ria (o/1)
 >? >
 >?
 q131<-ifelse(q13==1,0,ifelse(q13==2,1,ifelse(q13==3,1,
 >? > ifelse(q13==4,1,ifelse(q13==5,1,NA)))))
 >? > id3<-cbind(id3,q131)
 >? > id3$q131 <- as.factor(id3$q131)
 >? > str(id3)
 >? >
 >? > tp1 <- glm(q131 ~ q11 + q10+q12+edcat +
 >? q08+q06+ q14, family =
 >? > binomial(link =
 >? "logit"), data=id3,
 >? na.action="na.exclude")
 >? >
 >? tp1
 >? > hoslem.test(tp1$q131, fitted(tp1),
 >? g=10)
 >? >
 >? >
 >? >
 >? >
 >? --------------------------------------------
 >? > Em qui, 30/4/15, John Kane <jrkrideau at inbox.com>
 >? escreveu:
 >? >
 >? >
 >? Assunto: Re: [R] help - hoslem.test
 >? >
 >? Para: "PIKAL Petr" <petr.pikal at precheza.cz>,
 >? "Luciane Maria Pilotto"
 >? >

 >? "r-help at r-project.org"
 >? <r-help at r-
 >? > project.org>
 >? >
 >? Data: Quinta-feira, 30 de Abril de 2015, 11:51
 >? >
 >? >? Kevin Thorpe
 >? pointed out
 >? >? to me that there is a
 >? dropbox link at the very bottom of the
 >? >? post that I missed. :(
 >? >
 >? >? I
 >? >? just downloaded it, read it in and it
 >? looks fine.
 >? >
 >? >? John
 >? Kane
 >? >? Kingston ON Canada
 >? >
 >? >
 >? >? > -----Original
 >? >? Message-----
 >? >? >
 >? From: petr.pikal at precheza.cz
 >? >? > Sent: Thu, 30 Apr 2015 14:25:23
 >? +0000

 >? >? r-help at r-project.org
 >? >? > Subject: Re: [R] help -
 >? hoslem.test
 >? >? >
 >? >? > Hi
 >? >? >
 >? >? > I agree with John
 >? >? >
 >? >? > Just
 >? small
 >? >? refinements in lines
 >? >? >
 >? >? >>
 >? -----Original Message-----
 >? >
 >? >>> -----Original Message-----

 >? >? >>> Sent: Thu, 30 Apr 2015
 >? 04:24:32
 >? >? -0700
 >? >
 >? >>> To: r-help at r-project.org,
 >? >? jrkrideau at inbox.com
 >? >? >>> Subject: RE: [R] help -
 >? >? hoslem.test
 >? >
 >? >>>
 >? >? >>>
 >? load("id3.rda")
 >? >? >>
 >? And what is this?
 >? >? >>
 >? >? >> We do not
 >? >? have access to your office or
 computer
 >? hard disc.
 >? >? >>
 >? >? >> Please read
 >? >? http://stackoverflow.com/questions/5963269/how-to-make-a-
 >? >? >>
 great-r-reproducible-example,
 >? see
 >? >? ?dput for sending data?
 >? >? >>
 >? >? >>
 >? It is very unlikely anyone here can
 >? >
 >? help if we have no data.
 >? >? >>
 >? >? >>
 >? >
 >? >>>
 >? >? attach(id3)
 >? >? >
 >? >? > Do
 >? >? not use attach. It prevents from
 >? modifiyng id3.
 >? >? >
 >? >? >>>
 >? >
 >? >>> #transformando q13 em bin?ria
 >? >? >>>
 >? >
 >?
 q131<-ifelse(q13==1,1,ifelse(q13==2,2,ifelse(q13==3,2,
 >? >? >>>
 >? >
 >? ifelse(q13==4,2,ifelse(q13==5,2,NA)))))
 >? >? >
 >? >
 >? >? > q131 <- as.numeric(cut(q13,
 >? >? c(0,1.5,5)))
 >? >
 >? >
 >? >? >>
 >? >
 >? x<-1:7
 >? >? >> x
 >? >? >
 >? >? [1] 1 2 3 4
 >? 5 6 7
 >? >? >> as.numeric(cut(x,
 >? >? c(0,1.5,5)))
 >? >? >
 >? [1]? 1? 2? 2? 2? 2 NA
 >? >? NA
 >? >? >
 >? >
 >? >>>
 >? >
 >? id3<-cbind(id3,q131)
 >? >? >
 >? >? > rather dangerous in case id3 is
 >? not
 >? >? data.frame but matrix
 >? >? >
 >? >? >>>
 >? id3$q131 <-
 >? >? as.factor(id3$q131)
 >? >? >>>
 >? >
 >? >>> tp1 <- glm(q131 ~ q11 +
 >? >? q10+q12+edcat + q08+q06+ q14, family
 >? =
 >? >? >>> binomial(link =
 >? >? "logit"), data=id3)
 >? >? >>>
 >? >
 >? tp1
 >? >? >>>
 >? >? >>>
 >? library(ResourceSelection)
 >? >
 >? >>> hoslem.test(tp1$q131, fitted(tp1),
 >? >? g=10)
 >? >? >
 >? >? > hoslem.test
 >? >
 >? expects x to be a numeric vector of observations,
 binary
 >? >? > (0/1).
 >? >? >
 >? If I
 >? >? understand correctly tp1$q131
 >? have values 1, 2 or NA.
 >? >? >
 >? >? > Cheers
 >? >? >
 >? Petr
 >? >? >
 >? >
 >? >>>
 >? >? >>>
 >? >? dataframe: https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0
 >? >? >>>
 >? >
 >? >>>
 >? >? >>>
 >? >
 >?
 __________________________________________________
 >? >? >>> Luciane Maria Pilotto
 >? >? >>> Mestre e Doutoranda em
 >? Sa?de
 >? >? Bucal Coletiva - FO/UFRGS
 >? >? >>> NDE
 >? >
 >? Odontologia - UNIVATES
 >? >
 >? >>>
 >? >? Telefone: (51)
 >? 84512344
 >? >? >>>
 >? >? >>>
 >? >
 >? --------------------------------------------
 >? >? >>> Em qui, 30/4/15, John
 Kane
 >? <jrkrideau at inbox.com>
 >? >? escreveu:
 >? >
 >? >>>
 >? >? >>>? Assunto:
 >? RE: [R] help -
 >? >? hoslem.test
 >? >? >>>? Para:

 >? >? >>> r-help at r-project.org
 >? >? >>>? Data: Quinta-feira,
 30 de
 >? Abril
 >? >? de 2015, 7:52
 >? >? >>>
 >? >
 >? >>>? http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-
 >? >? >> reproducible-example
 >? >? >>>
 >? >
 >? >>>
 >? >? John Kane
 >? >? >>>? Kingston ON
 >? >? Canada
 >? >
 >? >>>
 >? >? >>>
 >? >? >>>
 >? >? >
 >? -----Original Message-----
 >? >

 >? >? >>>? > Sent: Wed, 29
 Apr
 >? 2015
 >? >? 18:45:26 -0700
 >? >? >>>? > To: r-help at r-project.org
 >? >? >>>? > Subject: [R]
 help
 >? -
 >? >? hoslem.test
 >? >
 >? >>>? >
 >? >? >>>
 >? > Hello,
 >? >? >>>? >
 >? >? >>>? > I'm working
 >? with
 >? >? >>>? ordinal logistic
 >? regression
 >? >? model (polr) and would
 >? like
 >? >? >>>
 >? >? > to test the proportional odds
 >? assumption.
 >? >? >>>? For this,
 >? I ran the binary
 >? >? >>>? >
 >? logistic
 >? >? >>>? regressions
 >? with varying
 >? >? cutpoints on the
 >? dependent
 >? >? >>>
 >? >? variable, as
 >? >
 >? >>>? > described
 >? >? in the
 >? following
 >? >? >>>? commands.
 >? >? When running the test of Hosmer and
 >? >? >>>? > Lemeshow
 >? (hoslem.test) for
 >? >? residuals gives
 >? >? >>>? error.
 >? >? >>>? >
 >? >? >>>? > Thanks,
 >? >? >>>? > Luciane
 >? >? >>>? >
 >? >? >>>? >
 >? >? >>>
 >? >
 >? ______________________________________________
 >? >? >>>? > R-help at r-project.org
 >? >? >>>? mailing list -- To
 >? UNSUBSCRIBE
 >? >? and more, see
 >? >? >>>? > https://stat.ethz.ch/mailman/listinfo/r-help
 >? >? >>>? > PLEASE do read
 the
 >? posting
 >? >? guide
 >? >
 >? >>>? > http://www.R-project.org/posting-guide.html
 >? >? >>>? > and provide
 >? commented,
 >? >? minimal,
 >? >? >>>? self-contained,
 >? >? reproducible code.
 >? >? >>>
 >? >
 >

 ________________________________
 Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou
 d?v?rn? a jsou ur?eny pouze jeho adres?t?m.
 Jestli?e jste obdr?el(a) tento e-mail omylem, informujte
 laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu
 i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu.
 Nejste-li zam??len?m adres?tem tohoto emailu, nejste
 opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat,
 kop?rovat ?i zve?ej?ovat.
 Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu
 zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu.

 V p??pad?, ?e je tento e-mail sou??st? obchodn?ho
 jedn?n?:
 - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv
 jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu
 i bez uveden? d?vodu.
 - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku
 bezodkladn? p?ijmout; Odes?latel tohoto e-mailu
 (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
 s dodatkem ?i odchylkou.
 - trv? odes?latel na tom, ?e p??slu?n? smlouva je
 uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech
 jej?ch n?le?itostech.
 - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n
 uzav?rat za spole?nost ??dn? smlouvy s v?jimkou
 p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn?
 pov??en a takov? pov??en? nebo pln? moc byly
 adres?tovi tohoto emailu p??padn? osob?, kterou
 adres?t zastupuje, p?edlo?eny nebo jejich existence je
 adres?tovi ?i osob? j?m zastoupen? zn?m?.

 This e-mail and any documents attached to it may be
 confidential and are intended only for its intended
 recipients.
 If you received this e-mail by mistake, please immediately
 inform its sender. Delete the contents of this e-mail with
 all attachments and its copies from your system.
 If you are not the intended recipient of this e-mail, you
 are not authorized to use, disseminate, copy or disclose
 this e-mail in any manner.
 The sender of this e-mail shall not be liable for any
 possible damage caused by modifications of the e-mail or by
 delay with transfer of the email.

 In case that this e-mail forms part of business dealings:
 - the sender reserves the right to end negotiations about
 entering into a contract in any time, for any reason, and
 without stating any reasoning.
 - if the e-mail contains an offer, the recipient is entitled
 to immediately accept such offer; The sender of this e-mail
 (offer) excludes any acceptance of the offer on the part of
 the recipient containing any amendment or variation.
 - the sender insists on that the respective contract is
 concluded only upon an express mutual agreement on all its
 aspects.
 - the sender of this e-mail informs that he/she is not
 authorized to enter into any contracts on behalf of the
 company except for cases in which he/she is expressly
 authorized to do so in writing, and such authorization or
 power of attorney is submitted to the recipient or the
 person represented by the recipient, or the existence of
 such authorization is known to the recipient of the person
 represented by the recipient.